Hello every one,
I am not able save the pdb file, after I broke the disulfide bond.
what I did was
1-loaded the pdb file
2-selected 3-button editing mode
3-selected the two atoms bonded by disulfide bond
4-unbond pk1,pk2
Now it shows the bond break, but when I was saving the file without
disulfide
The newest version of PyMOL (1.7.1.3)
solves this problem, just to announce you
to know that.
Thank you.
--
Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across
Hi,
This is because PyMOL does not read SSBOND records
in PDB files. Actually, PyMOL determines if a bond
is present based on atomic distances and CONECT records.
http://www.pymolwiki.org/index.php/Connect_mode
PyMOL does not write SSBOND records when saving a
PDB file.
Best regards,
Takanori
Hi guys
I wonder if you could help, I'm rendering this image:
http://qmviews.blogspot.ch/2014/05/illustrating-protein-structures.html
and I wonder if and how I could increase the thickness of the black
outlines?
Thanks for help
Martin
Hi Martin -
Try increasing the `ray_trace_gain` setting. Default value is 0.12, so maybe
try 1 or 2. If you go much higher, you’ll start to see additional lines or
spots.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On May 14,
That would seem to violate rule #1 of macromolecular depiction:
Never change the coordinates!
But then I can't imagine why one would want to not draw a disulfide bond
in a real protein structure, so maybe this is some kind of exercise
where it is not important to adhere to the experimental
